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Open Access Research article

Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta

Naoki Osada1*, Katsuyuki Hashimoto1, Yosuke Kameoka1, Makoto Hirata1, Reiko Tanuma1, Yasuhiro Uno2, Itsuro Inoue3, Munetomo Hida4, Yutaka Suzuki5, Sumio Sugano5, Keiji Terao6, Jun Kusuda1 and Ichiro Takahashi1

Author Affiliations

1 Department of Biomedical Resources, National Institute of Biomedical Innovation, Ibaraki, Japan

2 Pharmacokinetics and Bioanalysis Center, Shin Nippon Biomedical Laboratories, Ltd., Kainain, Japan

3 Division of Genetic Diagnosis, Institute of Medical Science, University of Tokyo, Tokyo, Japan

4 International Research and Educational Institute for Integrated Medical Sciences, Tokyo Women's Medical University, Tokyo, Japan

5 Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan

6 Tsukuba Primate Center for Medical Science, National Institute of Biomedical Innovation, Tsukuba, Japan

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BMC Genomics 2008, 9:90  doi:10.1186/1471-2164-9-90

Published: 24 February 2008



Cynomolgus macaques (Macaca fascicularis) are widely used as experimental animals in biomedical research and are closely related to other laboratory macaques, such as rhesus macaques (M. mulatta). We isolated 85,721 clones and determined 9407 full-insert sequences from cynomolgus monkey brain, testis, and liver. These sequences were annotated based on homology to human genes and stored in a database, QFbase webcite.


We found that 1024 transcripts did not represent any public human cDNA sequence and examined their expression using M. fascicularis oligonucleotide microarrays. Significant expression was detected for 544 (51%) of the unidentified transcripts. Moreover, we identified 226 genes containing exon alterations in the untranslated regions of the macaque transcripts, despite the highly conserved structure of the coding regions. Considering the polymorphism in the common ancestor of cynomolgus and rhesus macaques and the rate of PCR errors, the divergence time between the two species was estimated to be around 0.9 million years ago.


Transcript data from Old World monkeys provide a means not only to determine the evolutionary difference between human and non-human primates but also to unveil hidden transcripts in the human genome. Increasing the genomic resources and information of macaque monkeys will greatly contribute to the development of evolutionary biology and biomedical sciences.